Sir Brian Roche warned lockdown tolerance was waning, the vaccine rollout was failing Māori and MIQ was causing social and economic harm, a document dump released on Friday shows.
The esteemed advisor also told the Government the "current outbreak has revealed the very poor level of preparedness of hospitals for Delta".
Sir Brian reviewed the Delta outbreak and its impact on reopening the borders. He sent his advice to ministers on September 23 - two days after Auckland moved to alert level 3.
Tolerance and goodwill for lockdowns and closed borders were being challenged, Sir Brian warned.
"The current Delta outbreak has, to a significant extent, exposed urgent issues with respect to New Zealand's preparedness for reconnecting.
"Delta has fundamentally changed the model of preparedness and response and we must adapt accordingly. We do not have a do-nothing option."
High vaccination rates were a "critical first line of defence" and at least 90 per cent of New Zealanders needed to be vaccinated - but the vaccination rollout was "failing certain populations, most notably Māori", Sir Brian said.
"Addressing such disparities is an urgent priority."
A month later the Government announced a $120 million fund for Māori health providers.
The health system's ability to deal with Delta "was left wanting".
"The current Delta outbreak has exposed the shortfall in proper engagement of Māori and Pacific providers in the outbreak and overall response while it has also exposed the huge potential of proper engagement even when done at pace.
"Optimising engagement is an urgent priority."
Sir Brian also wanted the Government to begin opening the international border "to address escalating economic and social harms", but said before doing so there needed to be a means for vaccination verification, "coherent and fit-for-purpose plan" for MIQ alternatives with saliva and rapid antigen resting rolled out widely "as quickly as possible".
"Rapid antigen testing is a critical prerequisite - we cannot afford the delays in its introduction that have been experienced with saliva testing."
The Government only rolled out vaccine passes on November 17 and announced changes to MIQ alternatives and rapid antigen testing this week - two months after getting that advice.
To address the issues Sir Brian wanted a fit-for-purpose COVID agency or response unit because the current model "is failing and will fail" when the country reopens.
"We recommend that this unit is put in place before the end of the vaccination rollout as the current arrangements put the country at unnecessary risk."